VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 19 2002 - 09:45:59 CDT

Hi Jeroen,
  Psfgen, autoimd, etc are part of the plugins tree, so in order to have
them available in VMD, you need to make sure that you have a working
plugins directory wherever you installed the binary version that you
compiled from CVS. The ribbons warning you're getting is unrelated to
Surf, it is caused by VMD disliking some aspect of the molecular structure
you have loaded. It might be something as trivial as the way some atoms
in your structure are named. For the Surf binary, you either need to compile
your own from source, or use a binary such as we normally ship with the
regular binary distributions. From the information you posted below, it
sounds like the only problem you might be having with plugins is the
layout of your installed plugins directory. If you grab one of the binary
distributions and install it into /tmp or something like that, you can
see how the plugins directory needs to be laid out in order for VMD to
find it automatically.

  John

On Mon, Aug 19, 2002 at 10:33:41AM +0200, Jeroen Akershoek wrote:
> Hello,
>
> I just downloaded the latest VMD from CVS and having some problems getting
> it to visualise all our datasets correctly. A couple of things I noticed
> in the vmd output text: ( .. replacing some info lines)
>
> ..
> Automatic IMD package could not be loaded:
> can't find package psfgen
> ..
> Info) Opened sensor config file /usr/lib/vmd/.vmdsensors
> 0
> ..
> Info) Opened sensor config file /usr/lib/vmd/.vmdsensors
> 1
> ERROR) Warning: ribbons code encountered an unusual structure, geometry may not
> look as expected.
> ERROR) Warning: ribbons code encountered an unusual structure, geometry may not
> look as expected.
> ERROR) Warning: ribbons code encountered an unusual structure, geometry may not
> look as expected.
> ERROR) No SURF binary found; set the SURF_BIN environmental variable
> ERROR) to the location of your SURF executable.
> Info) Done.
> ERROR) Warning: ribbons code encountered an unusual structure, geometry may not
> look as expected.
>
> And indeed, it doesn't look as expected. I'm missing some surfaces (due
> to the missing SURF_BIN I take it) and the ribbons are missing some parts.
> However, I couldn't find something that resembled a SURF_BIN in the vmd
> directory. Closest I could find was a Surf.o in the vmd/LINUX directory.
> I guess something went wrong with the building, but I have no idea what.
>
> As for the psfgen, that's probably a path-thing, cause I have multiple
> psfgen directories in my $vmdlib/ (LINUX/psfgen1.2, LINUX/tcl/psfgen1.2,
> psfgen_plugin and psfgen).
>
> Hope you can help
>
> Regards
> Jeroen
> ----------------------------------------------
> Jeroen Akershoek, VR Specialist
> SARA Computing and Network Services
> tel: +31 20 5923000 fax: +31 20 6683167
>
> "I love deadlines. I like the whooshing sound they make as they fly by."
> -- Douglas Adams
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078